SourceForge meeting 2013-07-24
QUESTION: Is limiting channel activity to TRANSMEMBRANE TRANSPORT too restrictive?
Comes from a SF request from Rama for a new term to annotate Rpt2, an ATPase of the regulatory particle (RP) of the proteasome. PMID 11430818
The RP controls gating of the adjacent core proteasome (CP) channel, to allow entry of proteins into the CP for degradation. The obsolete term http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008575 describes the activity of Rpt2.
See also: PMID 11062564. A gated channel into the proteasome core particle.
[Term] id: GO:0015267 name: channel activity namespace: molecular_function def: "Catalysis of energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-] synonym: "alpha-type channel activity" RELATED  synonym: "channel-forming toxin activity" RELATED  synonym: "channel/pore class transporter activity" EXACT  synonym: "nonselective channel activity" EXACT  synonym: "pore activity" BROAD  synonym: "pore class transporter activity" RELATED  xref: TC:1 is_a: GO:0022803 ! passive transmembrane transporter activity
Should we create a new broader channel activity term that isn't restricted to movement across a membrane?
Missing xps to metabolism terms
Could David and Tanya please fill us in about any consensus reached at JGI last week... what 'roles' do we NOT care about? ...pigment, xenobiotic...?
Can I go ahead with my suggested strategy?
'Response to' vs. 'cellular response to'
I have created several children of 'intrinsic apoptotic pathway' of the type 'int. apo. path. _in response to_ hypoxia/DNA damage/etc' and I have them mapping to the 'response to' terms, not the 'cellular response to'. I feel I should amend that. Comments?
Where are we with this please https://www.ebi.ac.uk/panda/jira/browse/GO-154
I have a related Jira ticket https://www.ebi.ac.uk/panda/jira/browse/GO-131, Jane and Tanya have CC and BP, anything I should do on mine?
Propagating via positive and negative regulation
David and Tanya, did you get to look at this at JGI last week?